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Zinc in PDB 2y0s: Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group

Enzymatic activity of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group

All present enzymatic activity of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group, PDB code: 2y0s was solved by M.Wojtas, B.Peralta, M.Ondiviela, M.Mogni, S.D.Bell, N.G.A.Abrescia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.86 / 3.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 129.330, 195.909, 212.451, 90.00, 105.73, 90.00
R / Rfree (%) 30 / 35.4

Other elements in 2y0s:

The structure of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 6 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group (pdb code 2y0s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group, PDB code: 2y0s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 2y0s

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Zinc binding site 1 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1880

b:1.0
occ:1.00
 SG A:CYS58 1.6 0.9 1.0
NE2 A:HIS71 1.9 1.0 1.0
SG A:CYS68 2.0 0.4 1.0
SG A:CYS61 2.0 0.5 1.0
O A:CYS68 2.6 0.3 1.0
CD2 A:HIS71 2.8 0.4 1.0
CE1 A:HIS71 2.9 0.1 1.0
CB A:CYS68 3.1 0.2 1.0
CB A:CYS58 3.2 0.8 1.0
C A:CYS68 3.3 0.2 1.0
CG2 A:THR60 3.6 99.0 1.0
CA A:CYS68 3.7 1.0 1.0
CB A:CYS61 3.8 0.5 1.0
CG A:HIS71 3.9 0.6 1.0
ND1 A:HIS71 3.9 0.1 1.0
N A:PRO69 4.4 58.8 1.0
N A:CYS61 4.4 0.8 1.0
CA A:CYS58 4.5 1.0 1.0
CA A:GLY50 4.7 0.6 1.0
CA A:CYS61 4.8 0.0 1.0
CA A:PRO69 4.9 57.9 1.0
C A:PRO69 4.9 58.5 1.0
O A:PRO69 4.9 60.9 1.0
N A:GLY62 5.0 0.7 1.0

Zinc binding site 2 out of 14 in 2y0s

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Zinc binding site 2 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1881

b:1.0
occ:1.00
 SG A:CYS98 0.7 0.2 1.0
SG A:CYS101 1.7 0.8 1.0
CB A:CYS98 2.1 0.8 1.0
SG A:CYS146 2.4 0.9 1.0
O A:VAL145 2.8 0.3 1.0
CB A:CYS101 2.9 0.8 1.0
C A:VAL145 3.3 0.3 1.0
CA A:CYS98 3.5 0.6 1.0
N A:VAL145 3.6 0.6 1.0
CB A:CYS146 3.8 0.8 1.0
CG1 A:VAL145 3.9 0.9 1.0
CA A:VAL145 3.9 0.1 1.0
N A:CYS146 3.9 0.5 1.0
N A:CYS101 4.0 0.5 1.0
O A:CYS98 4.0 0.7 1.0
C A:CYS98 4.0 0.5 1.0
CA A:CYS101 4.1 0.2 1.0
CA A:CYS146 4.2 0.9 1.0
CB A:VAL145 4.5 0.4 1.0
N A:CYS98 4.6 0.9 1.0
O A:GLY102 4.7 0.4 1.0
N A:GLN144 4.7 0.5 1.0
CB A:GLN144 4.7 0.2 1.0
C A:GLN144 4.7 0.6 1.0
C A:ARG100 4.8 0.0 1.0
N A:GLY102 4.8 0.5 1.0
C A:CYS101 4.9 0.3 1.0
O A:LYS142 4.9 0.3 1.0
CA A:GLN144 4.9 1.0 1.0
N A:ARG100 5.0 0.8 1.0

Zinc binding site 3 out of 14 in 2y0s

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Zinc binding site 3 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2123

b:1.0
occ:1.00
 SG B:CYS1067 1.9 0.2 1.0
SG B:CYS1064 2.0 0.2 1.0
CG1 B:ILE1084 2.7 0.6 1.0
CB B:ILE1084 2.9 0.9 1.0
SG B:CYS1082 3.0 0.0 1.0
CB B:CYS1067 3.1 0.6 1.0
CB B:CYS1064 3.6 99.8 1.0
CG2 B:ILE1084 3.7 0.2 1.0
N B:CYS1067 4.0 0.1 1.0
CA B:ILE1084 4.2 0.8 1.0
CD1 B:ILE1084 4.2 0.7 1.0
CA B:CYS1067 4.2 0.1 1.0
N B:ILE1084 4.3 0.9 1.0
OG B:SER1089 4.4 0.6 1.0
CB B:CYS1082 4.4 0.1 1.0
CB B:GLN1066 4.7 0.7 1.0
C B:ILE1084 4.9 0.5 1.0
O B:TYR1069 4.9 0.2 1.0
CA B:CYS1064 4.9 91.3 1.0

Zinc binding site 4 out of 14 in 2y0s

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Zinc binding site 4 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2124

b:1.0
occ:1.00
 OD1 B:ASN572 2.1 89.1 1.0
ND1 B:HIS570 2.1 83.3 1.0
CG B:HIS570 2.9 85.0 1.0
CG B:ASN572 3.0 87.7 1.0
CE1 B:HIS570 3.1 83.7 1.0
CB B:HIS570 3.2 85.3 1.0
ND2 B:ASN572 3.2 86.4 1.0
OE1 B:GLU622 3.5 65.0 1.0
CD2 B:HIS570 4.1 86.8 1.0
NE2 B:HIS570 4.1 85.8 1.0
NH1 B:ARG174 4.3 87.0 1.0
CA B:HIS570 4.3 87.9 1.0
CD B:GLU622 4.5 66.6 1.0
CB B:ASN572 4.5 87.6 1.0
N B:GLY527 4.7 1.0 1.0
C B:HIS570 4.8 87.6 1.0
CZ B:ARG174 4.8 85.8 1.0
CG B:GLU622 4.9 68.0 1.0
N B:VAL571 4.9 87.4 1.0

Zinc binding site 5 out of 14 in 2y0s

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Zinc binding site 5 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2125

b:1.0
occ:1.00
 OG1 B:THR420 2.1 54.9 1.0
OD2 B:ASP418 3.0 44.8 1.0
CB B:THR420 3.3 56.7 1.0
CA B:THR420 3.6 59.1 1.0
N B:THR420 3.8 60.3 1.0
CG B:ASP418 4.1 46.7 1.0
CG2 B:THR420 4.4 55.9 1.0
C B:ARG419 4.7 71.2 1.0
CB B:ASP418 4.8 47.7 1.0
N B:ARG419 4.9 70.7 1.0
OD1 B:ASP418 4.9 48.0 1.0

Zinc binding site 6 out of 14 in 2y0s

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Zinc binding site 6 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1065

b:0.9
occ:1.00
 SG N:CYS10 2.0 84.1 1.0
SG N:CYS45 2.1 0.2 1.0
SG N:CYS44 2.1 99.9 1.0
SG N:CYS7 2.3 57.3 1.0
N N:CYS45 2.3 87.7 1.0
CA N:CYS45 2.7 73.9 1.0
CB N:CYS45 2.8 85.6 1.0
C N:CYS44 2.9 69.1 1.0
CB N:CYS10 3.1 98.3 1.0
CB N:CYS44 3.1 91.6 1.0
CB N:CYS7 3.4 58.3 1.0
N N:CYS10 3.5 67.5 1.0
CA N:CYS44 3.6 88.0 1.0
O N:CYS44 3.6 57.2 1.0
CA N:CYS10 3.9 82.9 1.0
C N:CYS45 4.2 71.0 1.0
CB N:THR9 4.2 0.6 1.0
N N:CYS44 4.3 0.7 1.0
C N:THR9 4.5 98.3 1.0
N N:THR9 4.7 68.4 1.0
CA N:THR9 4.7 86.7 1.0
NH2 N:ARG47 4.8 58.0 1.0
N N:GLY11 4.8 58.8 1.0
CA N:CYS7 4.8 58.9 1.0
N N:ARG46 4.9 84.0 1.0
C N:CYS10 4.9 73.8 1.0
OG N:SER12 5.0 0.3 1.0
OG1 N:THR9 5.0 91.2 1.0

Zinc binding site 7 out of 14 in 2y0s

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Zinc binding site 7 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn1065

b:0.3
occ:1.00
 SG O:CYS44 2.1 0.1 1.0
SG O:CYS45 2.2 0.8 1.0
N O:CYS45 2.2 1.0 1.0
SG O:CYS10 2.2 0.0 1.0
SG O:CYS7 2.2 90.9 1.0
CA O:CYS45 2.5 0.5 1.0
CB O:CYS45 2.7 0.7 1.0
C O:CYS44 2.8 91.7 1.0
CB O:CYS44 3.1 92.0 1.0
CB O:CYS7 3.3 91.4 1.0
CB O:CYS10 3.3 0.7 1.0
O O:CYS44 3.5 91.5 1.0
CA O:CYS44 3.5 91.7 1.0
N O:CYS10 3.6 0.4 1.0
C O:CYS45 4.0 0.3 1.0
CA O:CYS10 4.1 0.5 1.0
N O:CYS44 4.2 0.7 1.0
CB O:THR9 4.3 95.1 1.0
NH2 O:ARG47 4.6 91.3 1.0
C O:THR9 4.7 0.1 1.0
N O:ARG46 4.7 0.6 1.0
N O:THR9 4.7 94.1 1.0
CA O:CYS7 4.7 91.4 1.0
CA O:THR9 4.8 95.9 1.0
O O:CYS45 4.8 0.9 1.0
N O:GLY11 4.9 91.8 1.0

Zinc binding site 8 out of 14 in 2y0s

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Zinc binding site 8 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1049

b:0.7
occ:1.00
 SG P:CYS29 1.9 0.1 1.0
SG P:CYS9 2.0 0.0 1.0
OG1 P:THR12 2.1 0.2 1.0
SG P:CYS26 2.3 0.9 1.0
CB P:CYS9 2.4 99.3 1.0
O P:THR12 3.3 1.0 1.0
CB P:THR12 3.4 0.8 1.0
CB P:CYS29 3.6 0.9 1.0
CA P:CYS9 3.9 86.0 1.0
CB P:CYS26 3.9 0.8 1.0
C P:THR12 4.2 0.7 1.0
CA P:THR12 4.2 0.1 1.0
O P:TYR28 4.3 0.7 1.0
CG2 P:THR12 4.4 0.8 1.0
CA P:CYS29 4.5 0.2 1.0
O P:TRP10 4.5 0.1 1.0
N P:THR12 4.6 0.7 1.0
OG1 P:THR14 4.6 87.4 1.0
N P:CYS9 4.7 86.1 1.0
O P:PRO27 4.7 95.2 1.0
C P:CYS9 4.7 81.4 1.0
N P:TRP10 4.8 0.7 1.0
CB P:THR14 4.9 85.5 1.0
C P:TYR28 4.9 0.0 1.0

Zinc binding site 9 out of 14 in 2y0s

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Zinc binding site 9 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn2123

b:1.0
occ:1.00
 SG R:CYS1064 2.0 0.1 1.0
SG R:CYS1067 2.1 0.9 1.0
CB R:ILE1084 3.1 0.2 1.0
CG1 R:ILE1084 3.1 0.3 1.0
SG R:CYS1082 3.2 0.3 1.0
CB R:CYS1067 3.4 0.1 1.0
CG2 R:ILE1084 3.7 0.4 1.0
CB R:CYS1064 3.7 0.6 1.0
OG R:SER1089 3.9 1.0 1.0
N R:CYS1067 4.0 0.3 1.0
CA R:CYS1067 4.3 0.1 1.0
CB R:GLN1066 4.3 0.8 1.0
CA R:ILE1084 4.4 0.8 1.0
OE1 R:GLN1066 4.5 0.1 1.0
CD1 R:ILE1084 4.6 0.9 1.0
CB R:CYS1082 4.7 0.4 1.0
N R:ILE1084 4.7 0.1 1.0
C R:GLN1066 4.9 0.5 1.0
N R:GLN1066 4.9 0.2 1.0
CA R:CYS1064 4.9 0.5 1.0
CA R:GLN1066 4.9 0.3 1.0
C R:ILE1084 5.0 0.7 1.0
CB R:SER1089 5.0 0.1 1.0

Zinc binding site 10 out of 14 in 2y0s

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Zinc binding site 10 out of 14 in the Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn2124

b:1.0
occ:1.00
 ND1 R:HIS570 2.1 76.7 1.0
OD1 R:ASN572 2.1 79.2 1.0
CG R:HIS570 3.0 76.6 1.0
CG R:ASN572 3.0 77.1 1.0
CE1 R:HIS570 3.1 76.9 1.0
ND2 R:ASN572 3.1 74.4 1.0
CB R:HIS570 3.2 76.6 1.0
OE1 R:GLU622 3.5 73.7 1.0
CD2 R:HIS570 4.1 76.8 1.0
NE2 R:HIS570 4.2 76.7 1.0
NH1 R:ARG174 4.2 0.3 1.0
CA R:HIS570 4.3 81.0 1.0
CD R:GLU622 4.4 73.3 1.0
CB R:ASN572 4.5 77.8 1.0
N R:GLY527 4.7 80.9 1.0
CZ R:ARG174 4.8 0.0 1.0
CG R:GLU622 4.9 73.5 1.0
C R:HIS570 4.9 81.7 1.0

Reference:

M.Wojtas, B.Peralta, M.Ondiviela, M.Mogni, S.D.Bell, N.G.Abrescia. Archaeal Rna Polymerase: the Influence of the Protruding Stalk in Crystal Packing and Preliminary Biophysical Analysis of the RPO13 Subunit. Biochem. Soc. Trans. V. 39 25 2011.
ISSN: ISSN 1470-8752
PubMed: 21265742
DOI: 10.1042/BST0390025
Page generated: Thu Oct 17 05:38:27 2024

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